Genetic Variant CCDC7:n.*443G>C (chr10-32511838-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000545067.6(CCDC7):n.*443G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000168 in 596,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0000017 ( 0 hom. )

Consequence

CCDC7
ENST00000545067.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.411

Publications

3 publications found

Variant links:

Genes affected

CCDC7 (HGNC:26533): (coiled-coil domain containing 7)

CCDC7 links:

C1DP1 (HGNC:31465): (C1D nuclear receptor corepressor pseudogene 1)

C1DP1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC7	NM_001395015.1 link	c.873-6107G>C		intron_variant	Intron 10 of 43	ENST00000639629.2	NP_001381944.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC7	ENST00000639629.2 link	c.873-6107G>C		intron_variant	Intron 10 of 43	5	NM_001395015.1	ENSP00000491655.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000168

AC:

AN:

596778

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

315354

show subpopulations

African (AFR)

AF:

0.0000632

AC:

AN:

15820

American (AMR)

AF:

0.00

AC:

AN:

29972

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17866

East Asian (EAS)

AF:

0.00

AC:

AN:

32218

South Asian (SAS)

AF:

0.00

AC:

AN:

56944

European-Finnish (FIN)

AF:

0.00

AC:

AN:

47412

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2380

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

362766

Other (OTH)

AF:

0.00

AC:

AN:

31400

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

1205

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

3.6

(source)

DANN

Benign

0.36

PhyloP100

0.41

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over